Kind of an age old argument on quality versus price. Some say you can save the money and buy a KLR but then you have to add in a decent amount of money to get the bike up to snuff.
The GS on the other hand has better brakes, more power, better suspension, is fuel injected, not to mention the new 650 is a twin where the KLR is a thumper.
It all comes down to what you want. Maybe if you list your ideal bike points we could help you decide.
2013 Super Tenere